Given that an object imaged with the use of a scanning microscope tool is rarely uniform in thickness, determining the best-focus imaging condition across a large area of the object remains problematic and typically is based on data collected as a result of multiple through-focus scans of the object. The determination of the optimal number of such through-focus scans is a matter of chance in absence of precise information about the thickness distribution of the object across the area being imaged. As a result, both the overall process of imaging remains not optimized and the quality of the procured image of the object suffers, as at least some of the portions of the image are blurred due to less than optimal positioning of the objective with respect to an element of the object being imaged. Accordingly, there remains a need in method and system facilitating an automatic determination of a minimum number of through-focus scans that may be required to predict an optimal position of the focal plane of the objective with respect to the object such that imaging of the entire object produces an image with minimum blur.